Open AccessSidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.
Author(s) -
Bruce R. Gelin,
Martin Karplus
Publication year - 1975
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.72.6.2002
Subject(s) - chemistry , tyrosine , phenylalanine , amino acid , trypsin , aromatic amino acids , crystallography , ring (chemistry) , rotation (mathematics) , trypsin inhibitor , nuclear magnetic resonance , computational chemistry , biochemistry , organic chemistry , physics , enzyme , geometry , mathematics
Conformational potentials of sidechains in the bovine pancreatic trypsin inhibitor have been studied with an empirical energy function. Calculated minimumenergy positions are in excellent agreement with the x-ray structure for sidechains in the core or at the surface of the protein; as expected, angles for sidechains that are directed out into the solvent do not agree with the calculated values. The contributions to the potentials are analyzed and compared with the potentials for the free amino acid. Although there is a large restriction in the available conformational space due to nonbonded interactions, the minimum energy positions in the protein are close to those of the free amino acid; the significance of this result is discussed. To estimate the effective barriers for rotation of the aromatic rings (tyrosine and phenylalanine), calculations are done in which the protein is permitted to relax as a function of the ring orientation. Thr resulting barriers, which are much lowere than the rigid rotation barriers, are used to evaluate the rotation rates; comparison is made with the available nuclear magnetic resonance data.